Inhibitor oligonucleotides and their use for specific repression of a gene

ABSTRACT

The invention concerns a double-stranded oligonucleotide characterized in that it consists of two complementary oligonucleotide sequences forming a hybrid comprising each at one of their 3′ or 5′ ends one to five non-matched nucleotides forming single-stranded ends overlapping from the hybrid, one of said oligonucleotide sequences being substantially complementary of a target sequence belonging to a DNA or RNA molecule to be specifically repressed. The invention also concerns the use of said oligonucleotides in pharmaceutical compositions for treating cancers.

RELATED APPLICATIONS

This is a §371 of PCT/FR02/03843, filed Nov. 8, 2002 (now WO 03/040366 published May 15, 2003), which claims priority of FR 01/14549 filed Nov. 9, 2001 and FR 02/04474 filed Apr. 10, 2002.

FIELD OF THE INVENTION

This invention relates to the field of the genetic investigation and treatment of human pathologies, especially cancers and infectious diseases.

BACKGROUND

Known in the prior art are antisense oligonucleotide techniques making it possible to specifically inhibit a gene in mammal cells. These techniques are based on the introduction into cells a short oligonucleotide of DNA that is complementary to the target gene. This oligonucleotide induces the degradation of the messenger RNA (mRNA) transcribed by the target gene. Another the antisense technique comprises introducing into a cell a DNA oligonucleotide which forms a triple strand with the target gene. The formation of this triple strand represses the gene by either blocking access for activating proteins, or in more sophisticated approaches, by inducing degradation of the gene. None of these approaches appear to be based on a cellular mechanism existing in the cells of mammals, and they are not very effective. In fact, the clinical use of antisense has been reduced to a few rare cases, and it was believed that there was no possible use for oligonucleotides forming triple strands.

Interference RNA which is also designated “RNA′inh” or “RNAi” or cosuppression, has been demonstrated in plants. It was observed in plants that the introduction of a long double-strand RNA corresponding to a gene induced the specific and effective repression of the target gene. The mechanism of this interference comprises the degradation of the double-strand RNA into short oligonucleotide duplexes of 20 to 22 nucleotides.

The “RNA′inh” approach, more generally referred to according to the invention as inhibitory oligonucleotides or RNAi, is based on a cellular mechanism whose importance is underlined by its high degree of conservation since this mechanism is conserved throughout the plant and animal kingdoms and species, and has been demonstrated not only in plants but also in the worm Caenorhabditis elegans and yeasts, and mammals—humans and mice.

SUMMARY OF THE INVENTION

This invention relates to a method of determining the function of a gene or a family of genes implicated in a cellular process. This invention also relates to a method for repressing a harmful gene responsible for a pathology in humans or animals.

The invention also relates to active agents designed to implement the methods for determining gene function and repression of harmful genes that are responsible for a pathology in humans or animals. This invention also relates to compositions containing these active agents.

In the most general sense the embodiements of this invention utilize interference RNA, also known is “RNA′inh” or “RNAi” or cosuppression.

In one aspect, the inventors have now shown that the principles of “RNA′inh” can be applied to the genes of mammals, and more specifically to genes that play an important role in the control of the cellular destiny.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a schematic representation of the proteins RARα, PML and the associated fusion protein, PML-RARα.

FIG. 1B represents the results of transfections with an siRNA directed against PML-RARα.

FIG. 2 pertains to the inhibition of the expression of VEGF by siRNA directed against this protein and the consequences of this inhibition.

FIG. 2A represents the immunodetection of VEGF in the cJ4 or LNCaP cells transfected by the control siRNA or a siRNA directed against VEGF.

FIG. 2B represents the quantification using ELISA of VEGF in conditioned medium of cj4 cells transfected by the control siRNA or the siRNA VEGF as a function of time after transfection.

FIG. 2C represents the growth curve in nude mice of tumors stemming from the subcutaneous injection of 10⁶ cells of cJ4 that is not transfected, transfected by the control siRNA or the siRNA VEGF.

FIG. 2D represents the appearance of the tumors on day 7 after injection of the cells.

FIG. 2E represents the immunodetection of VEGF in tumors stemming from the injection of cJ4 cells transfected with the control siRNA or the siRNA VEGF after 12 days of development in vivo.

FIG. 3 shows the effect of inhibition by a siRNA specific of the expression of a transcription factor, HIF1α, on the transcriptional response to hypoxia. It also shows the measurement of the activity of a reporter VEGF luciferase in response to hypoxia in CJ4cells that are not transfected, by the control siRNA or by the siRNA directed against HIF1α.

FIG. 4 shows the inhibition by siRNA specific of the expression of the androgen receptor in the cells and functional consequences of these inhibitions.

FIG. 4A represents the detection by immunoblot of the expression of the androgen receptor 48 h after transfection of the LNCaP cells by a control siRNA or a siRNA directed against the androgen receptor (AR).

FIG. 4B represents the measurement of the activity of a reporter 4×ARE luciferase to R1881 in various clones of the line LNCaP not transfected, or transfected by control siRNA or by siRNA AR.

FIG. 4C represents the comparison of the response to R1881 of LNCaP cells that were not transfected (100%), and LNCaP cells transfected by a control siRNA, a siRNA directed against the androgen receptor (AR) or a siRNA recognizing specifically a punctiform mutation present in the androgen receptor of the line LNCaP.

FIG. 4D represents the growth in nude mice of tumors resulting from the subcutaneous injection of LNCaP cells transfected by a control siRNA or by a siRNA directed against the androgen receptor.

FIG. 4E represents the growth of LNCaP tumors in mice having received on the 40^(th) day after implantation of the cells an intravenous injection in the tail vein of 2 μg of siRNA directed against VEGF or of control siRNA.

FIG. 4F represents the growth of LNCaP tumors in mice having received on the 34^(th) and 40^(th) days after implantation of the tumor cells an intraperitoneal injection of 2 μg of siRNA directed against the androgen receptor or control siRNA.

FIG. 5 shows the inhibition of the expression of wild or mutant forms of p53 by siRNAs and the functional consequences of these inhibitions.

FIG. 5A represents the sequence of human p53 protein.

FIG. 5B represents the specific, dose-dependent inhibition by the siRNAs of the expression of wild or mutant forms of p53 transfected in cells not initially expressing it.

FIG. 5C represents the specific inhibition by siRNAs of the simultaneous or not simultaneous expression of wild or mutant forms of p53 transfected in cells not initially expressing it.

FIG. 5D represents the inhibition of the expression of wild endogenous p53 or a mutant form of 53 transfected by siRNA.

FIG. 5E represents the effect of the inhibition of p53 by siRNAs on the resistance to genotoxic stress.

FIGS. 5F, G, H and I represent the inhibition of the expression of a mutant form of p53 in the cells of a patient with Li-Fraumeni cancer syndrome at the level of the mRNA (5G) and the expression of the protein by immunoblot (GF) or in indirect immunofluorescence (5H) and the consequences on the resistance of these cells to genotoxic stress.

FIG. 5J shows the inhibition by the siRNAs specific of the dependent transfection of the wild or mutant forms of p53.

FIG. 5K shows the inhibition of the expression of one of the target genes of p53, p21, inhibitory protein of cellular proliferation, by the coexpression of mutant forms of p53 and the restoration of this expression by treatment of the cells with a siRNA inhibiting the synthesis of the mutant form of p53.

FIG. 6 shows the inhibition of the expression of the protein E6 of the human papilloma virus HPV by specific siRNAs and the consequences of this inhibition.

FIG. 6A represents the sequence of the HPV protein.

FIG. 6B represents the effect of inhibition by siRNAs specific of the expression of protein E6 of HPV in cells that express this virus, on the expression of p53 and p21.

FIGS. 6C and 6D represent the effect of the inhibition of the expression of the protein E6 of HPV on the cell cycle.

FIG. 7 shows the use of hybrid siRNAs comprising DNA bases and RNA bases.

FIGS. 7A and 7B represent the effect of siRNAs DNA/RNA hybrids on the expression of the GFP expression by transfection of the cells.

FIG. 7C compares the effect of RNA/RNA, DNA/RNA and RNA/DNA siRNAs at constant dose on the inhibition of the transcription induced by the androgen receptor.

FIGS. 7D and 7E represent the effects of a substitution of RNA bases by DNA bases in the siRNA sequence inhibiting the synthesis of p53.

FIG. 8 shows the inhibition of luciferase in tumors expressing this enzyme by injection of siRNA via the subcutaneous, intratumoral, intraperitoneal or intravenous route.

DETAILED DESCRIPTION

In one aspect of the invention, the Applicants' demonstrate that the approach described in more detail herein is much more effective for specifically repressing genes as compared to the techniques employed in the prior art. Moreover, this approach can combine the advantages of antisense and the antigene properties. In one aspect, the Applicants have found that in plants cosuppression was effected at the post-transcriptional level on mature RNA and also at the transcriptional level, thus on the gene itself. In another aspect, the repression is transmitted from generation to generation and thus enables repression of a gene in a prolonged definitive manner.

Thus the invention has as one aspect a double-strand oligonucleotide to be used in an interference RNA (RNAi) process, that is comprised of two complementary oligonucleotide sequences each comprising at one of their 3′ or 5′ ends, one to five unpaired nucleotides forming single-strand ends extending beyond the hybrid, one of said oligonucleotide sequences being substantially complementary to a target sequence belonging to a target DNA or RNA molecule which it is desired to repress specifically. This DNA or RNA can be of any type, it can be, e.g., messenger or ribosomal RNA or in one aspect the DNA of a gene.

Each of the two complementary oligonucleotide sequences advantageously comprises the same 3′ or 5′ end with five unpaired nucleotides forming single-strand ends extending beyond the hybrid.

In one embodiement, the two oligonucleotide sequences are advantageously substantially the same size.

Because of the base-pairing law, we designate distinctions by oligonucleotide of the invention wherein one or the other of the double-strand oligonucleotide sequences of the invention that is complementary to a target sequence belonging to a DNA or RNA molecule that is specifically repressed, can be either a single or double strand.

The oligonucleotides of the invention can be of a ribonucleotide, deoxyribonucleotide or mixed nature. In a preferred embodiement the complementary oligonucleotide of the target sequence, also designated antisense strain, is comprised primarily of a ribonucleotide. The sense strain can be of a ribonucleotide, deoxyribonucleotide or mixed nature. Examples of oligonucleotides of the invention of type RNA/RNA or DNA/RNA are given in the experimental part below.

In one preferred embodiement, the RNA/RNA hybrids are more stable than the DNA/DNA or DNA/RNA hybrids and much more stable than the single-strand nucleic acids used in the antisense strategies.

The term oligonucleotide is also understood to mean a polynucleotide of 2 to 100, more generally of 5 to 50, nucleotides of the ribonucleotide, deoxyribonucleotide or mixed type.

The part of the oligonucleotide sequence that is hybridized and complementary to the target sequence preferably is of a size comprised between 15 and 25 nucleotides, most preferably from 20 to 23 nucleotides.

The double-strand oligonucleotides of the invention comprise, preferably at the 3′ end of each strand, from 1 to 5 nucleotides, preferably from 2 to 3 nucleotides, and most preferably 2 nucleotides extending beyond the hybrid. These nucleotides extending beyond the hybrid can be complementary to or not complementary to the target sequence. Thus, in a particular form of implementation of the invention, the nucleotides extending beyond the hybrid are any nucleotides, e.g., thymines.

It is possible to represent a double-strand oligonucleotide of the invention in the following manner, i wherein each hyphen corresponds to a nucleotide and wherein each strand comprises at its 3′ end two thymines extending beyond the hybrid: 5′ --------------------TT3′ 3′TT--------------------5′

The sequence of the oligonucleotides of the invention is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene which it is desired to repress specifically. Although preference is given to oligonucleotides perfectly complementary to the target sequence, the term “substantially complementary” is understood to refer to the fact that the oligonucleotide sequences can comprise several nucleotides mutated in relation to the target sequence as long as the repressive properties of the targeted gene are not changed. Thus, an oligonucleotide sequence of the invention can comprise from 1 to 3 mutated nucleotides.

These mutated nucleotides can thus be those extending beyond the hybrid or nucleotides within the oligonucleotide sequence.

In one aspect of the invention, an oligonucleotide of the can be a perfect hybrid or contain one or more mismatches within the double strand. Nevertheless, it is preferable that part of the oligonucleotide sequence, which is hybridized, be perfectly complementary to the target sequence whereas the nucleotides extending beyond the hybrid can be of any type and especially thymines.

The term “perfectly complementary” is understood to mean that the oligonucleotide of the invention is complementary to a sequence that belongs to a DNA or RNA of a mutated gene. The oligonucleotides of the invention can thereby enable discrimination between the sequence of the wild gene and the mutated gene present a particular value both in the analysis of the genes as well as in the therapeutic uses of the oligonucleotides of the invention.

The oligonucleotides of the invention are generally comprised of natural nucleotide bases (A, T, G, C, U) but they can also be comprised of modified nucleotides or nucleotides bearing reactive groups or bridging agents or intercalating agents that can react with the target sequence complementary to the oligonucleotide.

The oligonucleotides of the invention can be prepared by the conventional methods for the chemical or biological synthesis of oligonucleotides.

The invention also relates to oligonucleotides coupled to substances promoting or enabling their penetration, targeting, or addressing into cells. These substances can for example include lipids, proteins, polypeptides, peptides or any other natural or synthetic substance. In fact, the oligonucleotides of the invention are intended to be internalized in the cells and, advantageously in certain cases, into the nucleus of cells where they interact with nucleic acid molecules of nucleic acids bearing the oligonucleotide target sequence. Similarly, it can be of value to promote their penetration into a particular tissue such as a tumor, bone, etc.

The oligonucleotides of the invention are useful for repressing in an effective and specific manner a gene or a set of genes, thus allowing for the treatment of numerous human pathologies. They can also be used as a research tool for the investigation and the comprehension of the gene function. The invention thus, has as one object pharmaceutical compositions comprising an oligonucleotide or a set of different nucleotides and the use of these oligonucleotides, alone or coupled to transport substances, such as a drug.

The oligonucleotides can be employed in ex vivo applications, e.g., during grafting. Thus, the oligonucleotides can be transfected into the cells, especially tumor cells, which will then be injected or they can be injected into tissues. For example, the oligonucleotides can be injected into already developed tumors via the local, systemic or aerosol route, etc. with vectorization agents.

The oligonucleotides will be used at adequate concentrations in relation to the application and the form of administration employed with suitable pharmaceutical excipients. Depending on the nature of the oligonucleotides (DNA/RNA or RNA/RNA), different doses could be used in order to obtain the desired biological effect.

The oligonucleotides of the invention are also useful as diagnostic tools making it possible to establish in vitro the genetic profile of a patient on the basis of a cell sample from the patient. The implementation of the oligonucleotides of the invention in such an analysis method makes it possible to know or to anticipate the response of the cancerous cells of this patient and to establish a personalized treatment or to adjust the treatment of a patient.

The oligonucleotides of the invention present multiple advantages compared to the conventional chemotherapeutic agents:

-   -   The RNA-RNA hybrids are more stable than the DNA-DNA or DNA-RNA         hybrids and much more stable than the single-strand nucleic         acids used in the antisense strategies.     -   Since they constitute natural compounds, there is no fear of any         immunological reactions or drug-related intolerance.     -   The transfection experiments performed in the framework of the         invention show a better penetration of the RNAi into the tumor         cells than that obtained with plasmids. This point is essential         in the case of tumor cells which are generally very difficult to         transfect.     -   The experiments involving systemic injection of siRNAs in vivo         show a very good penetration of these molecules into the         tissues.     -   It is easy to mix multiple RNAi with each other in order to take         as targets multiple cellular genes at the same time.

In one embodiement, the oligonucleotides of the invention and the compositions that contain them are useful for the treatment or prevention of infectious or viral diseases, such as AIDS, and the nonconventional infectious diseases, BSE and Creutzfeldt-Jakob disease. In one preferred embodiement, the oligonucleotides are suitable for treating the viral diseases at the origin of cancers. The table below presents examples of viruses implicated in cancerous pathologies in humans. TABLE 1 Virus Type of associated human cancer Hepatitis B virus Carcinoma of the liver (HBV) Epstein-Barr virus Burkitt's lymphoma, nasopharyngeal cancer, (EBV) Hodgkins's disease, non-Hodgkins lymphoma, gastric cancer, breast cancer) Human herpes virus Kaposi's sarcoma (KS), primary effusion 8 or HHV-8/KSHV lymphoma (PEL), multicentric Castleman's disease (MCD) HPV Neck of the uterus, head, neck, skin, nasopharynx Lymphocyte T virus Type T leukemia (HTLV) Hepatitis C virus Carcinoma of the liver (HCV)

The oligonucleotides of the invention and the compositions containing them are also useful for the treatment or prevention of diseases linked to hypervascularization such as age-linked macular degeneration, tumoral angiogenesis, diabetic retinopathies, psoriasis and rheumatoid arthritis.

The research studies performed in the framework of the invention showed that these oligonucleotides are suitable for repressing harmful genes implicated in canceration and thus most particularly useful for the treatment or prevention of cancers and oncologic diseases in general.

An ideal anticancer treatment should lead to the death of the tumor cell while avoiding resistance phenomena. Cell death can be obtained by:

-   -   Inhibition of cellular division, blocking the cell cycle,     -   Induction of the apoptosis of the tumor cells,     -   Induction of senescence,     -   Induction of necrosis,     -   Induction of differentiation. In this case, the treatment causes         the cell to return to a non-cancerous state.

Thus, the invention relates in one preferred embodiement to an oligonucleotide or a set of different oligonucleotides each containing an oligonucleotide sequence complementary to a target sequence belonging to a molecule of DNA or messenger DNA of a gene whose repression induces apoptosis, or senescence or necrosis or the differentiation of the tumor cells or prevents their division or more than one of these phenomena.

Induction of apoptosis of tumor cells is based on the fact that the function of numerous cellular genes (e.g., members of the family BCL2, BCL XL) is to protect the cells from apoptosis. The loss of expression of these genes induced by RNAi enables passage into apoptosis.

Cell death can also be induced by the loss of adhesion of the cells to the matrix (anoikis). This effect can be obtained by disturbing the balance between proteases and protease inhibitors in the tumors and their stromal environment. This disturbance can also diminish the capacities of tumor cells to invade healthy tissues and metastasize. The siRNAs can thus be used to prevent the synthesis of proteins of the families of the matrix metalloproteases (MMP), membranous matrix metalloproteases, their inhibitors (TIMPs) as well as activators of the protease inhibitors such as, PAI-1, and the proteases themselves such as, urokinase.

Induction of senescence is based on the fact that normal cells can only divide a limited number of times. This number is programmed, for example circa 50divisions for embryonic fibroblasts. Senesence can also be measured by the length of the telomeres, which get shorter as the cellular divisions advance. Below a certain size, the telomeres are no longer functional and the cell, incapable of division, enters into senescence. However, in germinal cells, this length is maintained constant by the action of an enzyme, telomerase. Telomerase is re-expressed in numerous cancers which enables the tumor cells to multiply indefinitely. A RNAi blocking the expression of telomerase would be without consequence on normal somatic cells and would lead tumor cells into senescence.

Blocking cell division also leads cells to senescence. Blockage can be obtained by inhibiting the essential cellular receptors. Depending on the nature of the cell, these receptors can belong to the class of receptors known as the growth factors (notably, EGF, SST2, PDGF, FGF), whether or not they are mutated, or to the nuclear receptors of hormones (notably, androgens, estrogens, glucocorticoids).

The hormone receptors are frequently mutated in cancers and the invention pertains in this case to the use of oligonucleotides recognizing the mutated forms of these receptors, which do not inhibit the synthesis of the wild forms. This makes it possible, for example, in the case of prostate carcinomas that have become resistant by mutation of the androgen receptor, to treat patients via the systemic route with siRNAs that block the synthesis of the mutated receptor without inducing the castration effects linked to the inhibition of the wild forms of the receptor in other organs. In fact, the Applicants' present an example using oligonucleotides recognizing mutated forms of the receptor.

The cell cycle can also be stopped by inhibiting the synthesis of proteins indispensable for its unfolding such as, for example, cyclins, cyclin-dependent kinases, DNA-replication enzymes, transcription factors such as E2F.

Induction of necrosis results from the requirement of the tumor cells for oxygen and nutriments. A tumor initially provides for its development from the preexisting vessels of the host. Beyond 1 to 2 mm in diameter, the cells located at the center of the tumor are in hypoxia. This hypoxia, via the intermediary of a proline hydroxylase, leads to the stabilization of the transcription factor Hif1α, whose sequence, SEQ ID NO. 59, is presented in the attachment, which by attaching itself on the HRE sequences in the promoters of its target genes triggers the hypoxic reaction. This reaction leads to the activation of about a hundred genes enabling activation, notably of the pathway of anaerobic glycolysis, which is the stress response, and angiogenesis. This latter mechanism activates the VEGF gene, whose sequence, SEQ ID NO. 60, is presented in the attachment, which is the principal tumoral angiogenic factor.

Thus in one embodiement, the oligonucleotides according to the invention block, for example, the expression of the transcription factor Hif1α or, for example, that of VEGF making the tumor cells incapable of mounting a hypoxic or angiogenic response. Angiogenesis is a mechanism that is normally repressed in the adult with the exception of the menstrual cycle (uterus ovaries). The inhibition of this mechanism therefore has few consequences for normal tissues.

In one embodiement, the invention relates to an oligonucleotide of which one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a molecule of DNA or messenger RNA of the gene coding:

-   -   the transcription factor Hif1α;     -   one or more isoforms of VEGF A or a member of the family of this         growth factor.

In certain cancers, the tumoral phenotype results from or is maintained by the expression of a protein normally absent from normal cells. This protein can result from the present or prior expression of a viral genome in the cell such as that of the papilloma virus (HPV) or the hepatitis B virus. This protein can also result from the mutation (punctiform, deletion, insertion) of a normal cellular gene. In this case, it is frequent that the mutated protein thereby produced possesses negative transdominant properties in relation to the normal protein. The specificity of the siRNA enables inhibition of the synthesis of the mutant protein without blocking the synthesis of the wild proteins. Two examples relating to the mutated form of the protein p53 and the androgen receptor are reported in the experimental section below.

The research studies performed in the framework of the invention demonstrate that these oligonucleotides are particularly suitable in one embodiement for repressing harmful genes implicated in canceration and more particularly those genes leading to the formation of fusion proteins in cancerous cells, such as the fusion protein PML-RAR alpha.

Thus in one embodiemnt, the invention relates to oligonucleotides whose sequence is complementary to a target sequence belonging to a gene resulting from a chromosomal translocation so as to inhibit the effects of the fusion protein expressed by this gene. Thus, the target sequence corresponds to the sequence of the junction of the fusion protein.

Table 2 of attachment A is a nonexhaustive list of the fusion proteins representing therapeutic or diagnostic targets for the oligonucleotides of the invention.

Targeting the junction between two genes with an oligonucleotide of the invention, for example, the two genes pml and rarα, makes it possible to attain specific inhibition of the fusion protein without affecting the biological role of the natural proteins which can be coded by the second allele. This form of implementation of the invention thus encompasses all of the fusion proteins implicated in carcinogenesis, particularly the leukemias. Further, the reciprocal forms as well as all of the variants of the fusion proteins cited in the attachment also constitute targets of the invention. In one embodiement, the invention thus relates to the use of oligonucleotides, as described above, for the preparation of a pharmaceutical composition intended for the treatment of diseases resulting from the expression of a fusion protein, and in particular for the treatment of cancers.

The present anticancer therapies target the cancerous cells, by different approaches that are employed in isolation or combined with each other (chemotherapy, surgery, radiotherapy, immunotherapy). The therapeutic failures are massively due to either the cells not having been reached by the treatment or, primarily, by cells that are mutated in response to the treatment. The capacity for mutation is greatly facilitated by the genetic instability of the tumor cells. The inhibition of tumor vascularization, depriving the cells of oxygen and nutriments, has in the past several years opened new therapeutic perspectives in cancer research. This strategy, which is complementary to the previously mentioned methods, targets the normal endothelial cell of the host, which is genetically stable and theoretically not likely to mutate. Numerous clinical trials directed at inhibiting tumoral angiogenesis via different approaches are underway worldwide. However, the initial reported results appear to be rather disappointing.

The inventors have demonstrated that tumors are capable of compensating for the effects of angiogenesis inhibitors by selecting subpopulations of cells secreting strong concentrations of pro angiogenic factors.

Tumors are not comprised of homogeneous cells with regard to their genetic expression. This is attested to by a very large number of studies in which immunolabeling was performed for a large variety of antigens in the tumors. Macroscopically, a tumor is frequently composed of regions that are highly vascularized alongside zones of necrosis or avascular regions.

This tumor heterogeneity promotes the ability of tumors to escape from the applied treatments, no matter what their nature. The greater the diversity of the genetic expression in a tumor, the greater the probability that there exists at least one cell capable of resisting an antitumor agent. It therefore appears to be essential to combine different strategies in order to first reduce the tumoral heterogeneity and avoid the escape phenomena.

In another embodiement, The invention relates to siRNAs that are inhibit the expression of genes responsible for the inactivation of p53 and their use in the treatment of cancers. p53 is the product of a tumor-suppressor gene or anti-oncogene, mutated in more than 50% of the tumors in humans. p53 is thus considered to be a guardian of the genome. It is activated in the cells in the case of genotoxic stress and participates in various processes including the induction of the programmed death process.

In 74% of the cases of monoallelic mutation, the inactivation of p53 is due to a punctiform mutation leading to the expression of protein that is mutated but of normal size. It is generally considered that the mutated version forms heteromers with the product of the wild allele on which it acts as a negative transdominant that blocks its activity. The mutant form also appears to have an oncogenous activity in itself. Thus, the mutated forms of p53 are capable of activating the gene MDR, which facilitates the resistance of the cancerous cells to chemotherapy. Moreover, the expression of mutants of p53 is associated with a stronger tumoral angiogenesis, probably because the mutant forms of p53 are no longer capable of stimulating the transcription of the gene of thrombospondin, one of the most powerful repressors of angiogenesis, and activate VEGF and bFGF, two powerful activators of angiogenesis. Moreover, the cells in which a mutated form of p53 is expressed lose various levels of regulation. In particular, they are no longer capable of initiating a programmed death process which constitutes one of the major protection processes against tumorigenesis. The restoration of wild type p53 activity in cultured tumor cells leads to the restoration of this cellular response. Thus, inhibiting the expression of the mutated forms of p53 represents a potentially powerful tool in anticancer therapy.

At present, there is no effective means for restoring p53 activity in human cancer cells. With regard to the cancers in which both alleles are inactivated, attempts to restore the p53 activity by gene therapy are envisaged. These approaches are complicated by the use of viral vectors that at present do not appear to be very effective.

Furthermore, it has been observed specifically in cervical cancers linked to infection by the HPV virus of the cells of the neck of the uterus that p53 can be inactivated by the overexpression of a viral protein. In fact, this virus codes for a protein, the protein E6, which inactivates p53. In this type of cancer, it is the inhibition of the protein E6 which could restore a wild p53 activity.

The invention has as one object providing new means enabling activation of p53 by inhibiting the expression of the genes responsible for its inactivation. The research studies performed in the framework of the present invention demonstrated that it was possible to repress in a very effective and very specific manner the expression of a mutant form of p53.

The invention pertains to oligonucleotides presenting a sequence complementary to a specific polynucleotide sequence of the gene of the mutated p53. Thus, these are oligonucleotides whose sequence bear a mutation in relation to the sequence of wild p53. The sequence of the wild gene of p53 is shown in the attached sequence listings as SEQ ID NO. 1. The different mutations that can intervene in the sequence of p53 are indicated in table 3 of attachment B at the end of the present description.

The mutations observed most frequently in cancerous pathologies are presented in table 4 below. TABLE 4 Position Wild p53 SEQ ID NO.1 R273H GAGGTGCGTGTTTGTGC SEQ ID NO. 61 R248Q gcaTgaaccggaggcccaT SEQ ID NO. 62 R248W gcaTgaaccggaggcccaT SEQ ID NO. 63 R249S gcaTgaaccggaggcccaT SEQ ID NO. 64 G245S CTGCATGGGCGGCATGAAC SEQ ID NO. 65 R282W TGGGAGAGACCGGCGCACA SEQ ID NO. 66 R175H TGTGAGGCACTGCCCCCAC SEQ ID NO. 67 C242S TAACAGTTCCTGCATGGGCG SEQ ID NO. 68 Position Mutated p53 R273H GAGGTGCATGTTTGTGC SEQ ID NO. 69 R248Q gcaTgaacCAgaggcccaT SEQ ID NO. 70 R248W GCATGAACTGGAGGC CAT SEQ ID NO. 71 R249S gcaTgaaccggagTcccaT SEQ ID NO. 72 G245S CTGCATGGGCAGAGCATGAAC SEQ ID NO. 73 R282W TGGGAGAGACTGGCGCACA SEQ ID NO. 74 R175H TGTGAGGCGCTGCCCCCAC SEQ ID NO. 75 C2425 TAACAGTTCCTCCATGGGCG SEQ ID NO. 76

Thus, the oligonucleotides according to one aspect of the invention are complementary to a target sequence belonging to the mutated gene of p53 carrying at least one of the mutations presented in table 3, and most particularly at least one of the mutations of table 4 above.

These oligonucleotides are capable of discriminating in an effective manner between the wild form and the mutated form of p3. The strategy is to block the expression of the mutated form to reactivate the wild form and induce in the cells a programmed death process for which the wild form is indispensable and/or to block any other process induced by the wild form of p53. Moreover, this discrimination capacity of the oligonucleotides of the invention makes it possible to not touch the cancerous cells and to spare the normal cells, which do not express this mutated form of p53.

The invention therefore also has as one object, the treatment or prevention of diseases induced by an inactivation of protein p53 particularly the cancers resulting from the expression of mutated p53 and the cancers resulting from the expression of inhibitory genes of p53. The invention also has as one object the prevention of the appearance of cancers in subjects expressing a mutated form of p53 as in the case of Li-Fraumeni cancer syndrome.

p53 can be inactivated via many distinct mechanisms. For example, in the majority of cervical cancers p53 is inactivated by E6, a protein coded by the human papilloma virus. E6 leads to the ubiquitinylation of p53 which leads to its degradation by the proteasome. In this case, the expression of p53 can be restored by inhibition of the expression of the protein E6. The aspects of this invention also relates to oligonucleotides presenting a sequence complementary to a specific polynucleotide sequence of the gene of the protein E6 of HPV. The sequence of the gene of the protein E6 of HPV is given in FIG. 6A as well as in the attached sequence listings as SEQ ID NO. 2.

As previously indicated, a strategy according to the invention has as its goal to block using RNAi the expression of the androgen receptor in carcinomas. The sequence of the androgen receptor is given in the attached sequence listings as SEQ ID NO. 77. In order to treat carcinomas before they became resistant or to treat those that had become resistant by amplification of the receptor without mutation, siRNA homologous to a region for which no mutation had been described in the data banks of mutations of the androgen receptors (indicated as siRNA AR) were used. In order to treat specifically the prostate carcinomas that had become androgen resistant by mutation, a sequencing of the mRNA coding for the receptor was performed in the patient's cells in order to devise a specific sequence of the mutation, making it possible to treat the patient without consequence for the normal cells. An example is presented for the use of siRNA recognizing specifically the mutation of the androgen receptor present in the cell line LNCaP (siRNA LNCaP). Consequently one aspect of the invention relates to oligonucleotides substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule coding the mutated or nonmutated androgen receptor. For example, the androgen receptor bearing at least one of the mutations presented in table 5 of attachment C. These oligonucleotides of the invention are specific to the androgen receptor and are useful for treating or preventing androgen-dependent diseases, such as, e.g., prostate cancer.

Other advantages and characteristics of the invention will become apparent from the examples below pertaining to:

-   -   Example 1: Inhibition of the protein PML-RARα associated with         acute promyelocytic leukemia (APL).     -   Example 2: Inhibition of the tumoral angiogenesis induced by         VEGF.     -   Example 3: Inhibition of the hypoxic response induced by HIF1α.     -   Example 4: Inhibition of the wild or mutant forms of the         androgen receptors in prostate carcinoma cells.     -   Example 5: Inhibition of the wild or mutant forms of the protein         p53.     -   Example 6: Inhibition of the viral protein E6.     -   Example 7: Use of DNA/RNA hybrids to inhibit the expression of         various proteins.     -   Example 8: In vivo administration of siRNA via different routes.

EXAMPLE 1 Inhibition of the Protein PML-RARα Associated with Acute Promyelocytic Leukemia (APL)

I—Introduction

Acute promyelocytic leukemia (APL) is due to the translocation t(15 ;17) on chromosome 15. In patients afflicted with APL, the receptor of retinoic acid (RARα) is fused to the protein PML (promyelocytic leukemia protein) thereby generating the fusion protein PML-RARα. Five fusion proteins bringing RARα into play have been identified to date. All of these leukemia types implicate the RARα receptor and are clinically similar, which suggests that the rupture of the transduction pathway of retinoic acid is crucial in the pathogenesis of APL leukemia.

The fusion protein PML-RARα retained the binding domains of the DNA and retinoic acid of the RARα. It has been shown that the fusion protein PML-RARα represses the expression of the target genes of retinoic acid and thereby also blocks the differentiation of the promyelocytic cells. Only the administration of pharmacological doses of retinoic acid remove transcriptional repression exerted by PML-RARα and restore cellular differentiation. Moreover, the protein portion PML of the fusion protein could also intervene in the mechanism of the blocking of the transduction pathway by retinoic acid. To the extent that PML functions as a growth inhibitor and an apoptotic agent and that it is required for the expression of certain genes induced by retinoic acid, the dominant negative effect of PML-RARα on PML could allow cells to acquire a growth capacity, a resistance to apoptosis and a termination of differentiation.

Cellular biology studies of PML have shown that this protein possesses a particular localization in the nucleus, in structures called nuclear bodies. It appears that these structures are in direct relation with the anti-oncogene role of PML. In malignant APL cells, the protein PML-RARα induces, by heterodimerization with PML, the delocalization of PML from the nuclear bodies to the micropunctuated structures that could correspond to PML-RARα anchorage sites on the chromatin. This delocalization could block the pro-apoptotic function of PML and its role in myeloid differentiation. Multiple research teams have shown that combined treatment with retinoic acid and AS₂O₃ on cell lines that express the fusion protein PML-RARα enable the degradation of the fusion proteins at the same time as a relocalization of PML on the nuclear bodies. This reorganization of the nuclear bodies restores the functions of PML and contributes to the restoration of differentiation.

Finally, the chimera protein PML-RARα would thus have a double dominant negative effect on RARα and on PML enabling the cells to escape from apoptosis and blocking the differentiation of the thereby transformed promyelocytes.

More than 98% of the patients suffering from APL leukemia present the translocation t(15 ;17) (q22 ;q21) which leads to the formation of fused genes PML-RARα α and RARα-PML. There exist two subtypes of fusion proteins PML-RARα: the S (short) fusions and the L (long) fusions). The long form of the fusion protein PML-RARα corresponding to a protein of 955 amino acids representing the predominantly expressed form, and thus was taken as model in this study (Attachments A, B and C). This protein comprises amino acids 1 to 552 of the protein PML fused with amino acids 59 to 462 of the α receptor of retinoic acid (RARα).

II—Preparation and Administration of the Oligonucleotides

Complementary RNA oligonucleotides corresponding to the sequence of the junction of the gene of the fusion protein, i.e., 10 nucleotides of the PML gene and 10 nucleotides of the RARα gene, were synthesized with addition of two deoxythymidines at 3′ (FIG. 1). These oligonucleotides were hybridized and the production of the double-strand oligonucleotide was verified on acrylamide gel.

The sequences of the PML-RAR and control siRNAs used (5′-3′) are presented below.

Control: FW: [CAUGUCAUGUGUCACAUCUC]RNA [TT]DNA (SEQ ID NO.3) REV: [GAGAUGUGACACAUGACAUG]RNA [TT]DNA (SEQ ID NO.4)

PR: Sense: [GGGGAGGCAGCCAUUGAGAC]RNA [TT]DNA (SEQ ID NO.5) Antisense: [GUCUCAAUGGCUGCCUCCCC]RNA [TT]DNA (SEQ ID NO.6)

III—Results

NIH3T3 fibroblasts were cotransfected with lipofectamine by an expression vector of the protein PML-RARα (100 ng) and by 500 ng of control siRNA (C) or siRNA directed against PML-RARα (PR). 48 h after transfection, a Western blot (FIG. 1B) was performed on the total cell extracts using an antibody which recognized the protein RARα, whole or in fusion protein form.

FIG. 1B shows that the transfection of siRNA PR very strongly inhibits the expression of fusion protein PML-RARα compared to the cells transfected with the control siRNA (C) without modifying the expression of the protein RARα.

EXAMPLE 2 Inhibition of Tumoral Angiogenesis by VEGF

I—Introduction

VEGF (vascular endothelial growth factor) is one of the most powerful angiogenic factors identified. These factors are overexpressed in numerous situations of pathological hypervascularization and notably in tumoral development. The inhibition of this angiogenesis enables blocking of tumor growth. The method has the goal of inhibiting tumoral angiogenesis by blocking the expression of one of these angiogenic factors, and as seen in this example, that of VEGF by the tumor cells.

II—Preparation and Administration of the Oligonucleotides

Two RNA oligonucleotides, complementary of a region of the coding sequence of human VEGF, conserved in the rat and the mice, were synthesized. Two deoxynucleotides (TT) were added at 3′:

Sequence of the RNAi VEGF: (SEQ ID NO.7) 5′[AUGUGAAUGCAGACCAAAGAA]RNA-TT [DNA] (SEQ ID NO.8) 5′[UUCUUUGGUCUGCAUUCACAU]RNA-TT [DNA]

Sequence of the control RNAi: (SEQ ID NO.9) 5′[CAUGUCAUGUGUCACAUCUC]RNA-TT [DNA] (SEQ ID NO. 10) 5′[GAGAUGUGACACAUGACAUg]RNA-TT [DNA]

These oligonucleotides or the control oligonucleotides, whose sequence presents no homology with the sequences stored in the data banks, were hybridized and transfected using the Polyfect kit (Qiagen) in the cells of a rat fibrosarcoma (cJ4) and in human cells of the prostate carcinoma LNCaP.

III—Results

48 h after transfection, an indirect immunofluorescence was performed to detect the expression of the protein in the cells. FIG. 2A shows a massive inhibition of the expression of VEGF.

In order to quantify this effect, quantitative determination of the VEGF in the transfected CJ4 cells in parallel with the control RNAi or with the RNAi VEGF was performed with ELISA (quantikine, R&D). The cells were incubated for 48 h prior to the quantitative determination in a medium containing 1% serum. The determination was performed 4 days and 6 days after transfection. Under these conditions, FIG. 2B shows an inhibition of the secretion of VEGF of 85% at 4 days and of 75% at 6 days and of 60% at 13 days in the cells transfected with the RNAi VEGF compared to the cells transfected with the control RNAi (FIG. 2B).

The effect of the inhibition of VEGF on the tumor cells was tested in vivo: 3 days after transfection, three groups of 4 female nude mice aged 4 weeks were injected subcutaneously at the rate of one million cells per mouse: the first group was injected with nontransfected cells, the second group was injected with cells transfected by the control RNAi, the third group was injected with cells transfected with RNAi VEGF. No selection of the transfected cells was performed before the injection.

Tumor growth was monitored by measuring the volume of the tumors at regular intervals (FIG. 2C).

FIGS. 2C and 2D do not show any significant difference between the sizes of the tumors in groups A and B. A very large reduction in the tumor volume was seen in group C. The appearance of the tumors, much whiter in group C (FIG. 2D), manifested a pronounced decrease in the tumoral vascularization. After sacrifice of the animals on day 12 after the injection, the tumors were dissected, fixed and immunodetection of VEGF was performed on sections of these tumors. There was seen a very strong reduction in the expression of VEGF in the tumors of group C compared to that of group B (FIG. 2E).

In another experiment, tumors were induced in male nude mice by injection of prostate carcinoma cells LNCaP. 40 days after injection, the volume of the tumors having reached 1 to 1.5 cm³, the mice were divided into two groups. The first group (4 mice) received an intravenous injection in the tail vein of 2 micrograms of control siRNA in 100 μl of PBS. The second group received an equivalent dose of siRNA VEGF under the same conditions. It was observed that the siRNA VEGF but not the control siRNA induced a transitory suspension in tumor growth (FIG. 4D).

EXAMPLE 3 Inhibition of the Hypoxic Reaction

I—Introduction

Certain tumors are capable of developing under strongly anoxic conditions. This is seen very frequently in tumors of regions that are very poorly vascularized. This weak sensitivity to hypoxia has two consequences: on the one hand, an antiangiogenic treatment has little chance of being effective on these tumors or these tumor subpopulations. On the other end, this weak vascularization makes it difficult to deliver the therapeutic molecules. The transcription factor Hif1α regulates the activity of more than 100 genes enabling the hypoxic response. The inhibition of this transcription factor in hypoxic tumors has the goal of blocking their growth.

II—Preparation of the Oligonucleotides

RNAi Hif1α (SEQ ID NO. 11) 5′[CAUGUGACCAUGAGGAAAUGA]RNA-TT [DNA] (SEQ ID NO. 12) 5′[UCAUUUCCUCAUGGUCACAUG]RNA-TT [DNA]

Control RNAi (SEQ ID NO. 13) 5′[GAUAGCAAUGACGAAUGCGUA]RNA-TT [DNA] (SEQ ID NO. 14) 5′[UACGCAUUCGUCAUUGCUAUC]RNA-TT [DNA] III—Results

The VEGF promoter contains a response element to the transcription factor Hif1α. In order to test in vitro the effect of an RNAi directed against Hif1α, we transfected cJ4 cells with a reporter vector VEGF-luciferase, alone or in combination with an RNAi Hif1α or control.

24 h after transfection, the cells were incubated for 18 h in medium without serum, with the addition in some cases of cobalt chloride 100 μM in order to produce hypoxic conditions; the luciferase activity was then measured.

FIG. 3 shows that a complete inhibition of the induction of the response of the promoter VEGF to hypoxia was observed when the cells were transfected with RNAi Hif1α but not with the control RNAi.

EXAMPLE 4 Inhibition of the Wild or Mutant Forms of the Androgen Receptors in Prostate Carcinomas

I—Introduction

The prostate carcinomas are the second cause of cancer mortality for men in the industrialized countries. They are the cause of more than 9500 deaths per year in France. The prostatic epithelial cells are dependent on androgens for their growth. Prostatic carcinomas are initially androgen dependent. Chemical castration thus initially can block the growth of the carcinoma. However, in all cases, these carcinomas become androgen independent and their prognosis becomes very negative. This androgen independence—depending on the individuals—is often due to a mutation of the receptor (conferring on it, for example, a response to estrogens or to glucocorticoids) or to an amplification of the receptor.

II—Preparation of the Oligonucleotides

Two RNA oligonucleotides complementary to a region of the coding sequence of the nonmutated human androgen receptor (AR) were synthesized. Two deoxynucleotides (TT) were added at 3′. In other experiments, siRNAs named LNCaP and specifically recognizing the mutation of the androgen receptor (T877A) in the cells of human prostate carcinoma LNCaP, were used.

AR: (SEQ ID NO. 15) 5′[GACUCAGCUGCCCCAUCCACG]RNA-TT [DNA] (SEQ ID NO. 16) 5′[CGUGGAUGGGGCAGCUGAGUC]RNA-TT [DNA]

Control: (SEQ ID NO. 17) 5′[GAUAGCAAUGACGAAUGCGUA]RNA-TT [DNA] (SEQ ID NO. 18) 5′[UACGCAUUCGUCAUUGCUAUC]RNA-TT [DNA]

LNCap: (SEQ ID NO. 19) 5′[GCAUCAGUUCGCUUUUGAC]RNA-TT [DNA] (SEQ ID NO. 20) 5′[GUCAAAAGCGAACUGAUGC]RNA-TT [DNA]

Multiple subclones of the human prostate carcinoma line LNCaP were used in this study. The original line, LNCaP, is androgen dependent. The cells LN70, obtained by repeated passages of the line LNCaP in vitro have a diminution in their response to androgens. The clone LNS5, obtained after passage of the animals in an animal, is androgen resistant.

III—Results

The LNCaP cells were transfected in vitro with siRNA AR or control siRNAs using the transfection agent Polyfect (Qiagen). 48 h after transfection, the cells were detached from their support. Half of the cells were used for performing a Western blot detection of the androgen receptor; the other half were put back in culture. The androgen receptor (band at 110 kDa) was no longer detectable by Western blot in the cells transfected by siRNA AR (FIG. 4A). The cells transfected by siRNA and put back in culture were found to be incapable of continuing their growth, to the opposite of the cells transfected by the control siRNA.

The level of response to the androgens was measured by transfecting different cellular clones of the lone LNCaP with a reporter vector placing the coding sequence of luciferase downstream of a minimal promoter flanked by 4 repetitions of the androgen response element (4×ARE). After transfection, the cells were incubated for 18 h in the absence of serum and in the presence or absence of a metabolically stable analogue of dihydrotesterone, R1881 (NEN). The ratio of the luciferase activities under these two conditions makes it possible to measure the level of response to the androgens of the reporter vector.

We measured the effect of the cotransfection in the control RNAi or RNAi AR cells on the response to the androgens of the different clones of the line LNCaP.

FIG. 4B shows a complete inhibition of the response to the androgens in the two androgen-sensitive clones: LNCaP and LNCaP p70. This method does not permit measurement of the response of the androgen-resistant clone LNS5 to the treatment by RNAi AR.

The androgen receptor present in the line LNCAP carries a mutation. We used two different siRNAs to inhibit its synthesis, the previously used siRNA AR and siRNA LNCaP specifically recognizing the mutation LNCaP. The response to the androgens was measured as in experiment 4B (FIG. 4C).

In order to study the effect of the inhibition of the expression of the androgen receptor on tumor growth in vivo of the prostate carcinoma cells, carcinoma cells LNCaP, transfected by a control siRNA (group A) or siRNA AR (group B) were injected subcutaneously in male nude mice. Tumor growth was monitored at regular intervals. It was seen that the tumors of the group B animals started growing later than those of group A and that the volume of the tumors of group B on the 48^(th) day was markedly smaller than that of the tumors of group A (FIG. 4D).

In another experiment, LNCaP cells were injected in male nude mice. When, on the 34^(th) day, the tumors had reached a volume comprised between 1.2 and 1.5 cm³, the mice received via the intraperitoneal route an injection of 2 μg of control siRNA or siRNA AR in 100 μl of PBS. This injection was repeated on the 40 day. It was seen that the administration of siRNA AR leads to a slowing down of the tumor growth (FIG. 4E).

EXAMPLE 5 Inhibition of the Wild or Mutant Forms of the Protein p53

I—Preparation of the Oligonucleotides

The three siRNAs whose sequences are presented below were prepared, one directed against the wild form of p3 and the other directed against the mutated form expressed in a patient which resulted in the establishment of a line.

This mutation corresponds to one of the three observed most frequently in human tumors.    - wild p53: (SEQ ID NO. 21) Sense: [ G CAUGAACCGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 22) Anti: [AUGGGCCUCCGGUUCAUG C ] RNA [TT] DNA    - p53 MT1 (r248w): (SEQ ID NO. 23) Sense: [GCAUGAACUGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 24) Anti: [AUGGGCCUCCAGUUCAUGC] RNA [TT] DNA    p53 MT2 (r248w): (SEQ ID NO. 25) Sense: [

UCAUGAACUGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 26) Anti: [AUGGGCCUCCAGUUUCAUG

A] RNA [TT] DNA

The underlined nucleotides in the wild p53 are those that mutated in the mutant form and which are in italics in the sequences of the mutated form of mutated p53 (p53 MT1 and MT2). The bases in bold above are mutations which were introduced in order to augment the specificity.

II—Results

As shown in FIG. 5B, the H1299-NCI cells, which do not express p53, were transfected (using lipofectamine) by expression vectors (400 ng) of wild p53 (WT) or mutated p53 (MT). siRNAs (in increasing doses: 0, 125 ng, 250 ng, 500 ng and 1000 ng) directed against the wild form (WT), the mutated form (MT1 and MT2) or an irrelevant siRNA (C) were transfected at the same time. The cells were collected 24 hours later and analyzed by Western blot with an antibody directed against p53.

As shown in FIG. 5C, the H1299-NCI cells, which did not express p53, were transfected (using lipofectamine) by expression vectors (400 ng) of wild p53 (WT), mutated p53 (MT) or a mixture of the two (WT+MT) as indicated. siRNAs (400 ng) directed against the wild form (WT), the mutated form (MT 1) or an irrelevant siRNA (C) were transfected at the same time. The cells were collected 24 hours later and analyzed by Western blot (ib: immunoblot) with cellular actin (Sigma) to monitor the amount of proteins used in the test.

As shown in FIG. 5D, U2OS cells (human osteosarcoma expressing a wild form of p53) were transfected in a stable manner either by a vector expressing a mutant form of p53 (R248W) or by the corresponding empty vector (pCDNA3). These lines were transfected by the indicated siRNAs and the expression of the indicated proteins was detected by Western blot.

In all cases, the siRNA directed against the mutated form of the protein inhibited the mutated form and the siRNA directed against the wild form inhibited the wild form. Furthermore, there was no crossed reaction because the siRNA directed against the wild form had no effect on the mutated form and vice versa. It should be noted that the expression of the mutant stabilizes the wild protein when it is co-expressed. Consequently, the inhibition of the mutant through its indirect effect brings the wild form to its base level without there being any inhibition of the expression of the protein.

As shown in FIG. 5E, the cells used in FIG. 5D were transfected by the indicated siRNAs. The cells were then subjected to a genotoxic stress by treatment with doxorubicin (200 ng/ml) for 24 h. FIG. 5E shows the analysis of the cell cycle of these cells by incorporation of propidium iodine and FACS analysis. The cells not transfected with the mutant form and thus only expressing the wild form (PCDNA cells) exhibited a high percentage of stopping at G1 in the presence of doxorubicin. The treatment of these cells with wild siRNA, diminishing the wild p53, reduced this stopping at G1. The cells expressing the mutated and wild form (R248W) stopped very little at G1 in the presence of doxorubicin, showing that the mutated form inhibits the activity of the wild form. When these cells were treated with siRNA MT1, they recovered a normal capacity (to compare with the untreated PCDNA controls) of stopping at G1, showing the restoration of the wild p53 activity in these cells.

As shown in FIGS. 5F, G and H, the MDA 087 cells (stemming from a patient suffering from a Li-Fraumeni cancer syndrome and expressing the mutant R248W) were transfected with a siRNA directed against the mutant form (MT1) of p53, or with an irrelevant siRNA (C) (1.6 μg). Expression of p53 was detected in these cells by Western blot (FIG. 5F); the messenger RNAs were measured by quantitative CR (Light Cycler, Roche) (FIG. 5G) or immunofluorescence (FIG. 5H).

The MDA 087 cells were transfected with a siRNA recognizing the wild form (WT) or the mutated form (MT1) of p53 or by a control siRNA then subjected to a genotoxic stress by treatment with doxorubicin (200 ng/ml) for 24 h. The expression of the mutant form of p53 was detected by Western blot in the cells. It can be seen that the cells having received siRNA MT1 were not capable of stabilizing p53 in response to doxorubicin (FIG. 51).

FIG. 5J shows the effect of the siRNAs MT1 and MT2 in cells that express the wild and mutated forms of p53. H1299-NCI cells, which do not express p53, were transfected (using lipofectamine) by a reporter vector carrying the gene of luciferase under control of a p53 response element and vectors of expression (400 ng) of the wild p53 (WT), mutated p53 (MT) or a mixture of the two (WT+MT), as indicated. siRNAs (400 ng) directed against the wild form (WT), the mutated form (MT1, MT2) or an irrelevant siRNA (C) were transfected at the same time. The cells were collected 24 hours later and analyzed for the expression of luciferase. Only the wild p53 activated the report vector and the co-expression of the mutant form inhibited this activity. The cotransfection of wild siRNA inhibited the expression of the wild protein and thus the residual activation of the reporter gene. The cotransfection of the siRNA MT 1 and MT2, in contrast, restored this activation by blocking selectively the expression of the mutated form and preventing the negative transdominant effect that it exerts on the wild form of p53.

FIG. 5K shows a similar result on the expression of one of the targets of p53, the inhibitory protein of cell proliferation p21, in cells treated as in FIG. 5F. The expression of p21, detected by Western blot, was activated by wild p53 and inhibited when the mutant was co-expressed. This inhibition was lifted in the presence of siRNA MT1.

EXAMPLE 6 Inhibition of the Viral Protein E6

I—Preparation of the Oligonucleotides

A siRNA directed against the HPV protein E6 was also prepared. It responds to the following sequence:    HPV-16-52 (SEQ ID NO. 27) Sense: 5′ [CCACAGUUAUGCACAUAUC] RNA [TT] DNA (SEQ ID NO. 28) Anti: 5′ [GCUCUGUGCAUAACUUGG] RNA [TT] DNA. II—Results

As shown in FIG. 6B, CasKi and SiHA cells, both expressing HPV protein E6, were transfected with the indicated siRNAs, treated or not treated as indicated with doxorubicin and analyzed by Western blot using the indicated antibodies. Treatment of the cells with siRNA E6 induced an augmentation in the expression of P53. This expression of p53 was manifested by an augmentation of the expression of the protein p21.

As shown in FIG. 6C, the cell cycle of the treated siHA cells as in FIG. 6B was analyzed by FACS. The figure represents a characteristic experiment. There was seen an augmentation of cells in phase G1 (FIG. 6D) in the cells treated with siRNA E6, an augmentation which was also seen in the cells when they were treated with doxorubicin.

EXAMPLE 7 Effect of the RNA/RNA Oligonucleotides and the DNA/RNA Hybrids

I—Introduction

The invention envisages the use of DNA/RNA hybrid oligonucleotides as alternative to the RNA/RNA oligonucleotides for inhibiting specifically the expression of a gene. In the case of the DNA/RNA hybrids, the sense strand is preferentially of a DNA nature and the antisense strand of a RNA nature. The other aspects related notably to the size of the oligonucleotides, the nature of the 3′ ends and the mode of synthesis are the same as for the RNA/RNA oligonucleotides. The applications of these DNA/RNA hybrids are identical to those previously described for the RNA/RNA siRNA especially with regard to the therapeutic and diagnostic applications and the validation of genes. However, the doses of oligonucleotides employed in order to obtain the same effects with the DNA/RNA hybrids and RNA/RNA can be different.

II—Preparation of the Oligonucleotides

The sense strand is the one whose sequence is identical to that of the messenger RNA. The antisense strand is the strand complementary to the sense strand. By convention, in a duplex the nature of the strands is indicated in the order sense/antisense. Thus, for example, a DNA/RNA hybrid, noted as D/R, is a oligonucleotide the sense strand of which is of a DNA nature and the antisense strand of which is of a RNA nature and of a sequence complementary to the messenger RNA.

In the experiments described, the oligonucleotides whose sequence is indicated below were used.

-   -   For the GFP:

GFP: (SEQ ID NO. 29) Sense: [GCAAGCTGACCCTGAAGTTCAT] DNA (SEQ ID NO. 30) Anti: [GAACUUCAGGGUCAGCUUGCCG] RNA

Control GFP: (SEQ ID NO. 31) Sense: [CAUGUCAUGUGUCACAUCUC] RNA [TT] DNA (SEQ ID NO. 32) Antisense: [GAGAUGUGACACAUGACAUG] RNA [TT] DNA

-   -   FOR THE LNCaP: The underlined bases below correspond to the         mutation of the androgen receptor expressed in the cells of         human prostate carcinoma (LNCaP).

LNCaP: (SEQ ID NO. 33) Sense: [GCATCAGTTCGCTTTTGACTT] DNA (SEQ ID NO. 34) [GCAUCAGUUCGCUUUUGAC] RNA-TT [DNA] (SEQ ID NO. 35) Antisense: [GTCAAAAGCGAACTGATGCTT] DNA (SEQ ID NO.36) [GUCAAAAGCGAACUGAUGC] RNA=TT [DNA]

Control LNCaP: (SEQ ID NO. 37) Sense: [GUUCGGUCUGCUUACACUA] RNA-TT [DNA] (SEQ ID NO. 38) Antisense: [UAGUGUAAGCAGACCGAAC] RNA-TT [DNA]

-   -   For p53:

The DNA of the hybrids noted H1 comprise RNA bases (U, underlined).

The mutation present in the MT1 oligonucleotides is indicated in italics.    WT: (SEQ ID NO. 39) Sense: 5′[GCAUGAACCGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 40) Anti: 5′[AUGGGCCUCCGGUUCAUGC] RNA [TT] DNA    WT H1 D/R: (SEQ ID NO. 41) Sense: 5′[GCA U GAACCGGAGGCCCA U TT] DNA (SEQ ID NO. 42) Anti: 5′[AUGGGCCUCCGGUUCAUGC] RNA [TT] DNA    WT H1 R/D: (SEQ ID NO. 43) Sense: 5′[GCAUGAACCGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 44) Anti: 5′[A U GGGCC U CCGG UU CA U GCTT] DNA    WT H2 R/D: (SEQ ID NO. 45) Sense: 5′[GCATGAACCGGAGGCCCATTT] DNA (SEQ ID NO. 46) Anti: 5′[AUGGGCCYCCGGUUCAYGC] RNA [TT] DNA    WT H2 R/D: (SEQ ID NO. 47) Sense: 5′[GCAUGAACCGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 48) Anti: 5′[ATGGGCCUTCCGGTTCATGCTT] DNA    MT1 (R248W) **: (SEQ ID NO. 49) Sense: 5′[GCAUGAACUGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 50) Anti: 5′[AUGGGCCUCC

AGUUCAUGC] RNA [TT] DNA    MT1 H1 D/R: (SEQ ID NO. 51) Sense: 5′[GCA U GAAC

UGGAGGCCCA U TT] DNA (SEQ ID NO. 52) Anti: 5′[AUGGGCCUCC

AGUUCAUGC] RNA [TT] DNA    MT1 H1 R/D: (SEQ ID NO. 53) Sense: 5′[GCAUGAACUGGAGGCCCAU] RNA [TT] DNA (SEQ ID NO. 54) Anti: 5′[A U GGGCC U CC

AG UU CA U GCTT] DNA    MT1 H2 DIR: (SEQ ID NO. 55) Sense: 5′[GCATGAAC

TGGAGGCCCATTT] DNA (SEQ ID NO. 56) Anti: 5′[AUGGGCCUCC

AGUUCAUGC] RNA [TT] DNA    MT1 H2 R/D: (SEQ ID NO. 57) Sense: 5′[GCATGAAC

TGGAGGCCCAT] RNA [TT] DNA (SEQ ID NO. 58) Anti: 5′[AUGGGCCUCC

AGUUCAUGCTT] DNA

II—Results

1) Inhibition of the GFP (Green Fluorescent Protein) by the DNA/RNA hybrids

The control siRNAs (RIR) or GFP (D/R) in increasing doses were introduced by transfection using the Polyfect kit in C2C12 mouse myoblasts at the same time as a GFP expression vector. The GFP level was monitored by Western blot (FIG. 7A) and by direct measurement of the fluorescence emitted by the GFP by means of a fluorometer (FIG. 7B). There was seen a strong inhibition (up to 80%) of the expression of GFP by the DNA/RNA hybrid siRNAs.

2) Inhibition of the Androgen Receptor by the DNA/RNA Hybrids

FIG. 7D shows that the H1 D/R hybrids are as effective as the RIR for inhibiting the expression of genes. H1299-NCI cells, which do not express p53, were transfected (using lipofectamine) by vectors of expression (400 ng) of wild p53 (WT), mutated p53 (MT) or a mixture of the two (WT+MT), as indicated. A CMV-GFP vector was also transfected as internal control. The siRNAs (400 ng) directed against the wild form (WT), the mutated form (MT) or an irrelevant siRNA (CTRL) were transfected at the same time. The cells were collected 24 hours later and analyzed by Western blot with an antibody directed against p53 (D01, Santa Cruz) or GFP (Santa-Cruz) to monitor the transfection efficacy. Note: the expression of the mutated form of the protein stabilizes the wild form.

FIG. 7E shows that the H2 D/R hybrids were as effective as the RIR for inhibiting the expression of the genes. The H1299-NCI cells, which do not express p53, were transfected (using lipofectamine) by expression vectors (400 ng) of wild p53 (WT), mutated p53 (MT) and a mixture of the two (WT+MT) as indicated. The siRNAs (400 ng) directed against the wild form (WT), the mutated form (MT) or an irrelevant siRNA (C) were transfected at the same time. The cells were collected 24 hours later and analyzed by Western blot with an antibody directed against p53 (D01, Santa Cruz).

EXAMPLE 8 Administration In Vivo of siRNA Via Different Routes

Tumor cells expressing luciferase in a stable manner were injected subcutaneously to nude mice (1 million cells in the right flank). On the 8^(th) day of tumor growth, the tumors having an average volume of 200 mm³ were injected either with control siRNAs (mixed sequence of HIF1α, see example 3) or with a siRNA directed against luciferase. The control siRNAs (3 μg/mouse) were injected in a volume of 50 μl in PBS via the subcutaneous route in the animal's flank.

The luciferase siRNAs were injected at the rate of 3 μg/mouse (3 animals in each group) in 50 μl of PBS via the subcutaneous route (sc), the intraperitoneal route (ip), the intravenous route (iv) (tail vein) or the intratumoral route (it). In this latter case, the luciferase siRNAs (3 μg/mouse) were diluted in only 20 μl of PBS.

Three days after injection of the siRNAs, the animals were sacrificed, the tumors were collected and homogenized with a Polytron grinder. Quantitative determination of the proteins and measurement of the luciferase activity in a luminometer were performed on the homogenates.

The results shown in FIG. 8 show the luciferase activity in relation to the quantity of protein.

-   Key to Attachment A, Table 2 (pages 44-46 of original French     document)     -   Tableau 2=Table 2     -   Annexe A=Attachment A -   Table headings: Disease/Fusion protein/Chromosomal     translocation/Reference Contents of table in English. -   Key to Attachment B, Table 3 (pages 47-56 of original French     document)     -   Tableau 3=Table 3     -   Annexe B=Attachment B     -   All text in English. -   Key to Attachment c, Table 5 (pages 57-100 of original French     document)     -   Tableau 5=Table 5     -   Annexe C=Attachment C     -   Table headings and contents in English. 

1-36. (canceled)
 37. A double-stranded oligonucleotide comprising two complementary oligonucleotide sequences forming a hybrid, wherein each oligonucleotide sequence comprises at one of their 3′ or 5′ ends one to five unpaired nucleotides forming single-strand ends extending beyond the hybrid, and wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or RNA molecule to be specifically repressed.
 38. The double-stranded oligonucleotide according to claim 37, wherein said DNA or RNA molecule to be specifically repressed is selected from the group consisting of messenger RNAs, ribosomal RNAs and genes.
 39. The double-stranded oligonucleotide according to claim 37, wherein each of the two complementary oligonucleotide sequences further comprises at said 3′ or 5′ ends identical one to five unpaired nucleotides forming single-strand ends extending beyond the hybrid.
 40. The double-stranded oligonucleotide according to claims 37, wherein the two complementary oligonucleotide sequences comprise at one of said 3′ or 5′ ends one to five unpaired nucleotides that are the same size.
 41. The double-stranded oligonucleotide according to claim 40, wherein the two complementary oligonucleotide sequences are the same size in absence of one to five unpaired nucleotides at one of said 3′ or 5′ ends.
 42. The double-stranded oligonucleotide according to claim 37, wherein the oligonucleotide sequence complementary to the target sequence comprises between 15 and 25 nucleotides.
 43. The double-stranded oligonucleotide according to claim 37, comprising a ribonucleotide, deoxyribonucleotide or a nucleotide having a mixed ribonucleotide and deoxyribonucleotide nature.
 44. The double-stranded oligonucleotide according to claim 37, wherein the oligonucleotide sequence complementary to the target sequence is an antisense strand, and wherein said antisense strand substantially comprises a ribonucleotide and wherein the second oligonucleotide sequence is a sense strand, comprising a ribonucleotide, deoxyribonucleotide or a mixture thereof
 45. The double-stranded oligonucleotide according to claim 37, comprising at the 3′ end of each of said oligonucleotide sequence 1 to 5 nucleotides extending beyond the hybrid.
 46. The double-stranded oligonucleotide according to claim 45, wherein the nucleotides extending beyond the hybrid are complementary to the target sequence.
 47. The double-stranded oligonucleotide according to claim 45, wherein the nucleotides extending beyond the hybrid are not complementary to the target sequence.
 48. The double-stranded oligonucleotide according to claim 37, wherein the nucleotides extending beyond the hybrid are thymines.
 49. The double-stranded oligonucleotide according to claim 37, coupled to substances enabling penetration of said double-stranded oligonucleotide into the cells.
 50. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene whose repression induces apoptosis, senescence, or necrosis in cells having said DNA or messenger RNA molecule.
 51. The double-stranded oligonucleotide according to claim 50, wherein said gene is selected from the group consisting of cellular genes from the family of BCL2, BCL XL, and genes from the family of matrix metalloproteases (MMP), membranous matrix metalloproteases, and MMP inhibitors (TIMPs).
 52. An The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene coding for transcription factor Hif1α.
 53. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene coding one or more isoforms of VEGF A.
 54. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a viral gene.
 55. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene coding a mutated protein.
 56. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene responsible for inactivation of p53.
 57. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule selected from the group consisting of genes coding mutated p53 and protein E6 of an human papilloma virus (HPV).
 58. The double-stranded oligonucleotide according to claim 57, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of the gene coding mutated p53, said gene having at least one mutation from Table
 3. 59. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence comprising a part of a gene resulting from a chromosomal translocation coding for a junction of a fusion protein, and wherein said oligonucleotide sequence binds to said target sequence to inhibit effects of said fusion protein expressed by said gene.
 60. The double-stranded oligonucleotide according to claim 59, wherein the fusion protein is selected from of the fusion proteins in Table
 2. 61. The double-stranded oligonucleotide according to claim 59, wherein the fusion protein is PML-RARα.
 62. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complementary to a target sequence belonging to a DNA or messenger RNA molecule of a gene coding a mutated or nonmutated androgen receptor.
 63. The double-stranded oligonucleotide according to claim 62, wherein the mutated androgen receptor comprises at least one of the mutations of Table 5, Annex C.
 64. A pharmaceutical composition suitable for identification of gene function comprising an active agent having at least one oligonucleotide according to claim
 37. 65. A method of treating a disease resulting from the expression of a harmful gene comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 66. A method of treating a disease resulting from expression of a fusion protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 59 to a mammal.
 67. The method of claim 65, wherein said disease is a cancer.
 68. A method of treating cancers resulting from expression of a gene coding for a mutated p53 protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 56 to a mammal.
 69. A method of treating cancers resulting from expression of a gene coding for HPV protein E6 comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 57 to a mammal.
 70. A method of treating AIDS, BSE or Creutzfeldt-Jakob comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 71. A method of treating a viral disease at the origin of cancers comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 72. A method of treating age-linked macular degeneration, tumoral angiogenesis, diabetic retinopathies, psoriasis or rheumatoid arthritis comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 73. The double-stranded oligonucleotide according to claim 37, wherein the oligonucleotide sequence complimentary to the target sequence comprises between 20 and 23 nucleotides.
 74. The double-stranded oligonucleotide according to claim 37, comprising at the 3′ and of each of said oligonucleotide sequence 2 to 3 nucleotides extending beyond the hybrid.
 75. The double-stranded oligonucleotide according to claim 37 coupled to substances enabling said double-stranded oligonucleotide to target a cell.
 76. The double-stranded oligonucleotide according to claim 37, wherein one of said oligonucleotide sequences is substantially complimentary to a target sequence belonging to a DNA or messenger RNA molecule of a gene whose repression induces differentiation of tumor cells and prevents tumor cell division.
 77. The double-stranded oligonucleotide according to claim 50, wherein said gene is selected from the group consisting of cellular genes BCL2, BCL XL, matrix metalloproteases (MMP), membranous matrix metalloproteases, and MMP inhibitors (TIMPs).
 78. The double-stranded oligonucleotide according to claim 75, wherein said gene is selected from the group consisting of cellular genes BCL2, BCL XL, matrix metalloproteases (MMP), membranous matrix metalloproteases, and MMP inhibitors (TIMPs).
 79. The double-stranded oligonucleotide according to claim 57, wherein one of said oligonucleotide sequences is substantially complimentary to a target sequence belonging to a DNA or messenger RNA molecule of the gene coding mutated p53, said gene having at least one mutation from Table
 4. 80. A pharmaceutical composition, comprising an active agent having at least one oligonucleotide according to claim
 37. 81. A method of preventing a disease resulting from the expression of a harmful gene comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 82. A method of preventing a disease resulting from expression of a fusion protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 59 to a mammal.
 83. A method of preventing a disease resulting from expression of a fusion protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 60 to a mammal.
 84. A method of preventing cancers resulting from expression of a gene coding for a mutated p53 protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 56 to a mammal.
 85. A method of treating cancers resulting from expression of a gene coding for a mutated p53 protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 57 to a mammal.
 86. A method of treating cancers resulting from expression of a gene coding for a mutated p53 protein comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 58 to a mammal.
 87. A method of preventing AIDS, BSE or Creutzfeldt-Jakob comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 88. A method of preventing a viral disease at the origin of cancers comprising: administering a therapeutically effective amount of a pharmaceutical composition having at least one oligonucleotide of claim 37 to a mammal.
 89. A method of preventing age-linked macular degeneration, tumoral angiogenesis, diabetic retinopathies, psoriasis or rheumatoid arthritis comprising: administering a pharmaceutical a therapeutically effective amount of composition having at least one oligonucleotide of claim 37 to a mammal. 